chr4-107934620-G-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_183075.3(CYP2U1):​c.490+2487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,862 control chromosomes in the GnomAD database, including 11,892 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 11892 hom., cov: 31)

Consequence

CYP2U1
NM_183075.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.56

Publications

9 publications found
Variant links:
Genes affected
CYP2U1 (HGNC:20582): (cytochrome P450 family 2 subfamily U member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This enzyme is a hydroxylase that metabolizes arachidonic acid, docosahexaenoic acid, and other long chain fatty acids. [provided by RefSeq, Jul 2008]
CYP2U1-AS1 (HGNC:54817): (CYP2U1 and SGMS2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CYP2U1NM_183075.3 linkc.490+2487G>A intron_variant Intron 1 of 4 ENST00000332884.11 NP_898898.1 Q7Z449-1
CYP2U1XM_005262717.2 linkc.544+2433G>A intron_variant Intron 1 of 4 XP_005262774.1
CYP2U1XM_005262720.2 linkc.490+2487G>A intron_variant Intron 1 of 3 XP_005262777.1
LOC107986298XR_001741784.2 linkn.205-24071C>T intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CYP2U1ENST00000332884.11 linkc.490+2487G>A intron_variant Intron 1 of 4 1 NM_183075.3 ENSP00000333212.6 Q7Z449-1

Frequencies

GnomAD3 genomes
AF:
0.388
AC:
58865
AN:
151744
Hom.:
11883
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.435
Gnomad AMI
AF:
0.314
Gnomad AMR
AF:
0.442
Gnomad ASJ
AF:
0.235
Gnomad EAS
AF:
0.684
Gnomad SAS
AF:
0.473
Gnomad FIN
AF:
0.398
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.327
Gnomad OTH
AF:
0.354
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.388
AC:
58902
AN:
151862
Hom.:
11892
Cov.:
31
AF XY:
0.397
AC XY:
29430
AN XY:
74224
show subpopulations
African (AFR)
AF:
0.435
AC:
17998
AN:
41388
American (AMR)
AF:
0.443
AC:
6761
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.235
AC:
816
AN:
3466
East Asian (EAS)
AF:
0.683
AC:
3525
AN:
5158
South Asian (SAS)
AF:
0.473
AC:
2278
AN:
4812
European-Finnish (FIN)
AF:
0.398
AC:
4186
AN:
10524
Middle Eastern (MID)
AF:
0.269
AC:
79
AN:
294
European-Non Finnish (NFE)
AF:
0.327
AC:
22233
AN:
67942
Other (OTH)
AF:
0.351
AC:
740
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1808
3615
5423
7230
9038
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
566
1132
1698
2264
2830
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.338
Hom.:
15628
Bravo
AF:
0.394
Asia WGS
AF:
0.516
AC:
1793
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
7.0
DANN
Benign
0.83
PhyloP100
1.6
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2131463; hg19: chr4-108855776; API